The distribution and abundance of intertidal organisms can be affected by short-term events, such as rain. We compared the effects of rain on intertidal mobile invertebrates in four common microhabitats with differing amounts of shelter (namely beds of oysters, coralline turf, bare patches and crevices) on sea walls in Sydney Harbour. There was an effect of rain on some, but not all taxa, although this was not consistent between locations or times. Effects of rain were observed for some species of gastropods and crustaceans, but not for polychaetes. Manipulative experiments using artificial rain indicated that rain, without the presence of run-off and independent of potential temporal confounding from differences in weather conditions, has a negative effect on abundances of amphipods in coralline turf. Pulse responses by mobile organisms to short-term rain events should be considered when designing experiments looking at temporal variability and processes responsible for observed patterns of distribution of marine organisms.